**2.1. Crystal structure of organic torsion helicoids**

In recent years, several different interesting organic compounds structures have been found by X-ray crystallography. Helicenes are an extremely attractive and interesting class of conjugated molecules currently investigated for optoelectronic applications "(Groen et al., 1971; Katz, 2000; Rajca et al., 2007; Schmuck, 2003; Urbano, 2003)". They combine the electronic properties afforded by their conjugated system with the chiroptical properties "(Bossi et al., 2009; Collins

& Vachon, 2006; Larsen et al., 1996)" afforded by their interesting and peculiar helix-like structure, resulting from the condensation of aromatic (and/or heteroaromatic) rings, all of them in *ortho* position. For example, the formula and crystal structures of tetrathia-[7]-helicene **1** are shown in Figures 1 and 2, respectively. The compound **1** has been synthesized in three step by starting material of benzo[1,2-*b*:4,3-*b*']dithiophene and is shown in Scheme 1 "(Maiorana et al., 2003)" and this compound showed second-order non-linear optical (NLO) properties and has been investigated (Clays et al., 2003). In particular, carbohelicenes only include benzene rings, and also in heterohelicenes one or more aromatic rings are heterocyclic (pyridine, thiophene, pyrrole and etc.) "(Miyasaka et al., 2005; Rajca et al., 2004)". With increasing number of condensed rings (typically, *n* > 4), the steric interference of the terminal rings forces the molecule to be a helicoidal form. For *n* > 4 the energetic barrier is such that the two enantiomers can be separated and stored "(Martin, 1974; Newman, et al., 1955, 1967; Newman & Lednicer, 1956; Newman & Chen, 1972)". Of course, the conjugation of π system decreases with decreasing of planarity; however, in longer helicenes π-stack interactions can also take place between overlapping rings "(Caronna et al., 2001; Liberko et al., 1993)". All helicenes (generally, *n* > 4) are chiral molecules and exhibit huge specific optical rotations "(Nuckolls et al., 1996, 1998)" since the chromophore itself, in this case the entire aromatic molecule, is inherently dissymmetric (right-hand or left-hand helix), having a twofold symmetry axis, *C*2, perpendicular to its cylindrical helix (in carbohelicenes), or inherently asymmetric (in heterohelicenes) "(Wynberg, 1971)".

**Figure 2.** The helicoid structures of unsubstituted tetrathia-[7]-helicene **1** and unsubstituted hexathia- [11]-helicene **3** "(Caronna et al., 2001)" with the labelling scheme adopted for structural discussion "(Bossi et al., 2009)".

**Scheme 1.** The synthesis of **1** from benzo[1,2-*b*:4,3-*b*']dithiophene as a starting material.

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asymmetric (in heterohelicenes) "(Wynberg, 1971)".

S S

**1**

**Figure 2.** The helicoid structures of unsubstituted tetrathia-[7]-helicene **1** and unsubstituted hexathia- [11]-helicene **3** "(Caronna et al., 2001)" with the labelling scheme adopted for structural discussion

**Figure 1.** Formula structures of **1** and **2**.

"(Bossi et al., 2009)".

S S

& Vachon, 2006; Larsen et al., 1996)" afforded by their interesting and peculiar helix-like structure, resulting from the condensation of aromatic (and/or heteroaromatic) rings, all of them in *ortho* position. For example, the formula and crystal structures of tetrathia-[7]-helicene **1** are shown in Figures 1 and 2, respectively. The compound **1** has been synthesized in three step by starting material of benzo[1,2-*b*:4,3-*b*']dithiophene and is shown in Scheme 1 "(Maiorana et al., 2003)" and this compound showed second-order non-linear optical (NLO) properties and has been investigated (Clays et al., 2003). In particular, carbohelicenes only include benzene rings, and also in heterohelicenes one or more aromatic rings are heterocyclic (pyridine, thiophene, pyrrole and etc.) "(Miyasaka et al., 2005; Rajca et al., 2004)". With increasing number of condensed rings (typically, *n* > 4), the steric interference of the terminal rings forces the molecule to be a helicoidal form. For *n* > 4 the energetic barrier is such that the two enantiomers can be separated and stored "(Martin, 1974; Newman, et al., 1955, 1967; Newman & Lednicer, 1956; Newman & Chen, 1972)". Of course, the conjugation of π system decreases with decreasing of planarity; however, in longer helicenes π-stack interactions can also take place between overlapping rings "(Caronna et al., 2001; Liberko et al., 1993)". All helicenes (generally, *n* > 4) are chiral molecules and exhibit huge specific optical rotations "(Nuckolls et al., 1996, 1998)" since the chromophore itself, in this case the entire aromatic molecule, is inherently dissymmetric (right-hand or left-hand helix), having a twofold symmetry axis, *C*2, perpendicular to its cylindrical helix (in carbohelicenes), or inherently

**2**

**Scheme 2.** Reaction mechanism for formation of **5** "Garcia et al., 2009)".

Tetrathia-[7]-helicene **1** have been used for the synthesis of organometallic complexes "(Garcia et al., 2009)". A series of organometallic complexes possessing tetrathia-[7]-helicene nitrile derivative ligands **5** as chromophores, has been synthesized and fully characterized by Garcia et al. "(Garcia et al., 2009)". This compound was analyzed by means of 1H NMR, FT-IR, UV–Vis and X-ray crystallography techniques. The spectroscopic data of this compound was shown with in order to evaluate the existence of electronic delocalization from the metal centre to the coordinated ligand to have some insight on the potentiality of this compound as non-linear optical molecular materials. Slow crystallization of compound **4** revealed an interesting isomerization of the helical ligand with formation of two carboncarbon bonds between the two terminal thiophenes, leading to the total closure of the helix **5**. The reaction mechanism for the formation of **5** is shown in Scheme 2. Crystal structure of **5** is shown in Figure 3. A selected bond length, angles and torsion angles for compound **5** is summarized in Table 1 "Garcia et al., 2009)".

Another example about helicenes is the hexahelicene **2** and its derivatives that is a chiral molecule "(Noroozi Pesyan, 2006; Smith & March, 2001)". A convenient route for the synthesis of [7]-helicene (**6a**) and [7]-bromohelicene (**6b**) is reported "(Liu et al., 1991)". The crystal structure of 6b is shown in Fig. 4. The crystal structure of **6b** and its unusual oxidation reaction product **7** (as a major product) has been reported "(Fuchter et al., 2012)" (Figure 4 and Scheme 3). Alternatively, compound **6** may be an option for a neutral helicenederived metallocene complex, since the seven-membered benzenoid rings give rise to a scaffold that completes one full turn of the helix with the two terminal rings being co-facial. It has been theoretically predicted and reported that the **6** has potential to bind some metal cation such as Cr, Mo, W, and Pt in a sandwich model "(Johansson & Patzschke, 2009)". Fuchter and co-workers "(Fuchter et al., 2012)" also reported the crystal structure of **7** that obtained via unusual oxidation rearrangement of **6**. In this structure, The bonds within the pyrenyl unit range between 1.3726(19) and 1.4388(14) Å with the exception of one outlier at 1.3512(18) Å for the C(26)–C(27) bond. The C=C double bonds in rings D and E are 1.3603(15) and 1.3417(16) Å respectively, and the C=O bond is 1.2419(14) Å. The structure of **7** revealed the dominant canonical form to have a pyrenyl group consisting of rings A, B, C and H linked by single bonds to a C–C=C–C=C–C=O unit to form rings D and E (Scheme 3). The pyrenyl unit is flat, the sixteen carbon atoms being coplanar. Ring I has four single bonds and two aromatic bonds, and has a folded conformation with the methylene carbon lying ca. 0.87 Åout of the plane of the other five carbons which are coplanar. Aryl ring G forming the five-membered ring J, links to ring I. The planes of the five coplanar atoms of ring I and the four coplanar atoms of ring J are inclined by ca. 108° to each other. The ring of E is slightly distorted in a boat-like fashion with the carbon shared just with ring D and that shared with rings I and J, out of the plane of the other four atoms which are coplanar to within ca. 0.01 Å.

The formula structure of Katz's helical ferrocene **8** is shown in Figure 5 "(Katz & Pesti, 1982; Sudhakar & Katz, 1986)".

**Figure 3.** Crystal structure of **5**.

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within ca. 0.01 Å.

Sudhakar & Katz, 1986)".

summarized in Table 1 "Garcia et al., 2009)".

Tetrathia-[7]-helicene **1** have been used for the synthesis of organometallic complexes "(Garcia et al., 2009)". A series of organometallic complexes possessing tetrathia-[7]-helicene nitrile derivative ligands **5** as chromophores, has been synthesized and fully characterized by Garcia et al. "(Garcia et al., 2009)". This compound was analyzed by means of 1H NMR, FT-IR, UV–Vis and X-ray crystallography techniques. The spectroscopic data of this compound was shown with in order to evaluate the existence of electronic delocalization from the metal centre to the coordinated ligand to have some insight on the potentiality of this compound as non-linear optical molecular materials. Slow crystallization of compound **4** revealed an interesting isomerization of the helical ligand with formation of two carboncarbon bonds between the two terminal thiophenes, leading to the total closure of the helix **5**. The reaction mechanism for the formation of **5** is shown in Scheme 2. Crystal structure of **5** is shown in Figure 3. A selected bond length, angles and torsion angles for compound **5** is

Another example about helicenes is the hexahelicene **2** and its derivatives that is a chiral molecule "(Noroozi Pesyan, 2006; Smith & March, 2001)". A convenient route for the synthesis of [7]-helicene (**6a**) and [7]-bromohelicene (**6b**) is reported "(Liu et al., 1991)". The crystal structure of 6b is shown in Fig. 4. The crystal structure of **6b** and its unusual oxidation reaction product **7** (as a major product) has been reported "(Fuchter et al., 2012)" (Figure 4 and Scheme 3). Alternatively, compound **6** may be an option for a neutral helicenederived metallocene complex, since the seven-membered benzenoid rings give rise to a scaffold that completes one full turn of the helix with the two terminal rings being co-facial. It has been theoretically predicted and reported that the **6** has potential to bind some metal cation such as Cr, Mo, W, and Pt in a sandwich model "(Johansson & Patzschke, 2009)". Fuchter and co-workers "(Fuchter et al., 2012)" also reported the crystal structure of **7** that obtained via unusual oxidation rearrangement of **6**. In this structure, The bonds within the pyrenyl unit range between 1.3726(19) and 1.4388(14) Å with the exception of one outlier at 1.3512(18) Å for the C(26)–C(27) bond. The C=C double bonds in rings D and E are 1.3603(15) and 1.3417(16) Å respectively, and the C=O bond is 1.2419(14) Å. The structure of **7** revealed the dominant canonical form to have a pyrenyl group consisting of rings A, B, C and H linked by single bonds to a C–C=C–C=C–C=O unit to form rings D and E (Scheme 3). The pyrenyl unit is flat, the sixteen carbon atoms being coplanar. Ring I has four single bonds and two aromatic bonds, and has a folded conformation with the methylene carbon lying ca. 0.87 Åout of the plane of the other five carbons which are coplanar. Aryl ring G forming the five-membered ring J, links to ring I. The planes of the five coplanar atoms of ring I and the four coplanar atoms of ring J are inclined by ca. 108° to each other. The ring of E is slightly distorted in a boat-like fashion with the carbon shared just with ring D and that shared with rings I and J, out of the plane of the other four atoms which are coplanar to

The formula structure of Katz's helical ferrocene **8** is shown in Figure 5 "(Katz & Pesti, 1982;


a Cp ring centroid.

**Table 1.** Selected bond distances and bond and torsion angles for compound **5** "(Garcia et al., 2009)".

**Scheme 3.** The formula structures of **6a** and **6b** and its unusual reaction for synthesis of **7a** (and also its structure).

**Figure 4.** Crystal structures of **6b** and **7a**.

**Figure 5.** The formula structure of Katz's helical ferrocene **8**.

Diazepinone dervatives are of pharmaceutical compounds. Another interesting helical diazepinone compound that is discussed in this section, is 1,9-dimethyl-4,5-dihydro-6*H*pyrido[3',2':4,5]thieno[2,3-*f*]pyrrolo[1,2-*a*][1,4]diazepin-6-one (**9**). This molecule show two crystallographically independent molecules that form the asymmetric unit of the structure are shown in Figure 6. The X-ray crystallographic analysis shows the molecular structure of the compound **9** and reveals an interesting fact that this structure features two stereochemically different molecules (**9A** and **9B**) that can be understood as different torsion helicoids (Figure 6). The compound has two stereoisomers (*R* and *S* conformers). In each structure the seven-membered diazepinone ring exhibits a boat conformation.

**Scheme 4.** Two possible different torsion helicoids of **9**.

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structure).

**Figure 4.** Crystal structures of **6b** and **7a**.

**Figure 5.** The formula structure of Katz's helical ferrocene **8**.

**Scheme 3.** The formula structures of **6a** and **6b** and its unusual reaction for synthesis of **7a** (and also its

**Figure 6.** Two independent molecules of **9** in the crystal studied.

The fused pyrido[3',2':4,5]thieno ring moiety has planar geometry. The C3–H3 bond is slightly off the fused pyrido[3',2':4,5]thieno ring plane. The hindrance repulsion between the hydrogen atom at C3 on pyridine ring and methyl group on pyrrole ring makes the molecule of **9** essentially non-planar (repulsion of C3–H3A with C15 and C3'–H3'B with C15' of methyl groups) (Scheme 4). The torsion angles between the pyrrole and thiophene rings in **9A** and **9B** are 45.7(6)° and –49.3(6)°, respectively "(Noroozi Pesyan, 2010)".

The –NH– group of each molecule (e.g*.* molecule **9A**) makes an intermolecular hydrogen bond to the C=O functional group of the molecule of another kind (molecule **9B**), and *vice versa*. For example, the intermolecular hydrogen bond N3–H3····O1' involves the N3 atom from molecule **9A** and O1' atom from the carbonyl group of molecule **9B**, and *vice versa* for N3'–H3'····O1 (Figure 7). The crystal packing diagram indicates zigzag hydrogen-bonded chains along the crystallographic axes with two distinct hydrogen bonds (Figure 7). The intermolecular hydrogen bonds play a principal and important role in the crystal packing diagram of **9** "(Noroozi Pesyan, 2010)".

**Figure 7.** Crystal packing diagram of **9** showing zigzag H-bonds (shown by dashed lines).

One of the most interesting helical primary structure is sown in Figure 8 has been reported by Fitjer et al. "(Fitjer et al., 2003)". Helical primary structures of spiro annelated rings are unknown in nature but have been articially produced, both in racemic and enantiomerically pure form. The formula structure of 1-cyclobutylidenespiro[3.3]heptane (**10**) as a starting material is shown in Scheme 5. The compound **10** yielded enantiomeric mixture of **11** and **12** in the presence of zinc and 2,2,2-trichloroacetyl chloride. Reductive dehalogenation of **11** and **12** then Wolff–Kishner reduction yielded the desired trispiro[3.0.0.3.2.2]tridecane [rac-(**15**), (symmetry, C2)]. The crystal structure of the camphanic acid derivative of **15** ((1*S*,5'*S*,10'*S*)-**16**) is shown in Figure 8 "(Fitjer et al., 2003)".

**Scheme 5.** Synthesis of the compounds trispiro[3.0.0.3.2.2]tridecane (**15**) and the formula structure of its derivative (1*S*,5'*S*,10'*S*)-**16** "(Fitjer et al., 2003)".

**Figure 8.** Crystal structure of **(1***S***,5'***S***,10'***S***)-16**.

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diagram of **9** "(Noroozi Pesyan, 2010)".

The fused pyrido[3',2':4,5]thieno ring moiety has planar geometry. The C3–H3 bond is slightly off the fused pyrido[3',2':4,5]thieno ring plane. The hindrance repulsion between the hydrogen atom at C3 on pyridine ring and methyl group on pyrrole ring makes the molecule of **9** essentially non-planar (repulsion of C3–H3A with C15 and C3'–H3'B with C15' of methyl groups) (Scheme 4). The torsion angles between the pyrrole and thiophene rings

The –NH– group of each molecule (e.g*.* molecule **9A**) makes an intermolecular hydrogen bond to the C=O functional group of the molecule of another kind (molecule **9B**), and *vice versa*. For example, the intermolecular hydrogen bond N3–H3····O1' involves the N3 atom from molecule **9A** and O1' atom from the carbonyl group of molecule **9B**, and *vice versa* for N3'–H3'····O1 (Figure 7). The crystal packing diagram indicates zigzag hydrogen-bonded chains along the crystallographic axes with two distinct hydrogen bonds (Figure 7). The intermolecular hydrogen bonds play a principal and important role in the crystal packing

in **9A** and **9B** are 45.7(6)° and –49.3(6)°, respectively "(Noroozi Pesyan, 2010)".

**Figure 7.** Crystal packing diagram of **9** showing zigzag H-bonds (shown by dashed lines).

One of the most interesting helical primary structure is sown in Figure 8 has been reported by Fitjer et al. "(Fitjer et al., 2003)". Helical primary structures of spiro annelated rings are unknown in nature but have been articially produced, both in racemic and enantiomerically pure form. The formula structure of 1-cyclobutylidenespiro[3.3]heptane (**10**) as a starting material is shown in Scheme 5. The compound **10** yielded enantiomeric mixture of **11** and **12** in the presence of zinc and 2,2,2-trichloroacetyl chloride. Reductive dehalogenation of **11** and **12** then Wolff–Kishner reduction yielded the desired trispiro[3.0.0.3.2.2]tridecane [rac-(**15**), (symmetry, C2)]. The crystal structure of the camphanic acid derivative of **15** ((1*S*,5'*S*,10'*S*)-**16**) is shown in Figure 8 "(Fitjer et al., 2003)".

Helquats, the family of *N*-heteroaromatic cations "(Arai & Hida, 1992)", recently were introduced helical dications that represent a missing structural link between helicenes and viologens"(Casado et al., 2008)". Specifically, basic [7]-helquat (**17**) "(Severa et al., 2010)" is a structural hybrid between [7]-helicene and a well-known herbicide diquat (Scheme 6). Synthesis of [7]-helquat (**17**) starts with bisquaternization of bis-isoquinoline precursor (**18**) with an excess of 3-butynyltriflate followed by the key metal catalyzed [2+2+2] cycloisomerization of the resulting triyne, formed **17** (Scheme 7).

**Scheme 6.** Structural relation of [7]-helquat (**17**) to [7]-helicene **6a** and herbicide diquat.

**Scheme 7.** Synthesis of **17** via one-pot bis-quaternization of **18**.

Recently, Nakano et al. have been reported the helical structure, λ5-phospha [7]-helicenes 9 phenyl-9*H*-naphtho[1,2-*e*]phenanthro[3,4-*b*]phosphindole-9-oxide (**21**) and its thio analogue 9-phenyl-9*H*-naphtho[1,2-*e*]phenanthro[3,4-*b*]phosphindole-9-sulfide (**22**) "(Nakano et al., 2012)". The formula structure of **21** and **22** and the crystal structure of **21** are shown in Fig. 10. Phospha [7]-helicenes **21** and **22** have more distorted structures than the other heterohelicenes. In the structure of **21**, the sums of the five dihedral angles that are derived from the seven C–C bonds [C(17)-C(17a)-C(17b)-C(17c), C(17a)-C(17b)-C(17c)-C-(17d), C(17b)-C(17c)-C(17d)-C(17e), C(17c)-C(17d)-C(17e)-C(17f), and C(17d)-C(17e)-C(17f)-C(1)] are 95.28 for **21** and 99.68 for **22**. These angles are larger than those of hetero[7]-helicenes **23–25** (79–88°). This case can be attributed to the large angles between the two double bonds of phosphole oxide (50°) and phosphole sulfide (50°) relative to furan (32°), pyrrole (35°), and thiophene (45°). Owing to the larger angle, a larger overlap of the two terminal benzene rings was occurred in the λ5-phospha[7]-helicenes, therefore, a stronger steric repulsion. These larger distortions in **21** and **22** explain the higher tolerance of **21** and **22** towards racemization.

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Helquats, the family of *N*-heteroaromatic cations "(Arai & Hida, 1992)", recently were introduced helical dications that represent a missing structural link between helicenes and viologens"(Casado et al., 2008)". Specifically, basic [7]-helquat (**17**) "(Severa et al., 2010)" is a structural hybrid between [7]-helicene and a well-known herbicide diquat (Scheme 6). Synthesis of [7]-helquat (**17**) starts with bisquaternization of bis-isoquinoline precursor (**18**) with an excess of 3-butynyltriflate followed by the key metal catalyzed [2+2+2]

cycloisomerization of the resulting triyne, formed **17** (Scheme 7).

**Scheme 7.** Synthesis of **17** via one-pot bis-quaternization of **18**.

**Scheme 6.** Structural relation of [7]-helquat (**17**) to [7]-helicene **6a** and herbicide diquat.

Recently, Nakano et al. have been reported the helical structure, λ5-phospha [7]-helicenes 9 phenyl-9*H*-naphtho[1,2-*e*]phenanthro[3,4-*b*]phosphindole-9-oxide (**21**) and its thio analogue 9-phenyl-9*H*-naphtho[1,2-*e*]phenanthro[3,4-*b*]phosphindole-9-sulfide (**22**) "(Nakano et al., 2012)". The formula structure of **21** and **22** and the crystal structure of **21** are shown in Fig. 10. Phospha [7]-helicenes **21** and **22** have more distorted structures than the other heterohelicenes. In the structure of **21**, the sums of the five dihedral angles that are derived from the seven C–C bonds [C(17)-C(17a)-C(17b)-C(17c), C(17a)-C(17b)-C(17c)-C-(17d), C(17b)-C(17c)-C(17d)-C(17e), C(17c)-C(17d)-C(17e)-C(17f), and C(17d)-C(17e)-C(17f)-C(1)] are 95.28 for **21** and 99.68 for **22**. These angles are larger than those of hetero[7]-helicenes **23–25** (79–88°). This case can be attributed to the large angles between the two double bonds of phosphole oxide (50°) and phosphole sulfide (50°) relative to furan (32°), pyrrole (35°), and thiophene (45°). Owing to the larger angle, a larger overlap of the two terminal benzene rings was occurred in the λ5-phospha[7]-helicenes, therefore, a stronger steric repulsion. These larger distortions in **21** and **22** explain the higher tolerance of **21** and **22** towards racemization.

**Figure 9.** Formula and X-ray single crystal structure of compounds **19** and **20** (Triflate counterions are omitted for clarity) "(Severa et al., 2010)".

**Figure 10.** Formula structures of λ5-Phospha[7]-helicenes **21** and **22** and crystal structure of **21** as representative.
